108 lines
4.1 KiB
Groff
108 lines
4.1 KiB
Groff
LAMMPS (27 Oct 2021)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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package omp 0
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using multi-threaded neighbor list subroutines
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# monolayer MoS2
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units metal
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boundary p p f
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processors * * 1
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atom_style full
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read_data single_layer_MoS2.data
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Reading data file ...
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triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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768 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.005 seconds
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mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
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mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
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########################## Define potentials ################################
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pair_style sw/mod/omp
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pair_coeff * * tmd.sw.mod Mo S S
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Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
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#########################################################################
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### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345
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############################
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# Output
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thermo 500
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thermo_style custom step etotal pe ke temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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fix thermostat all nve
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run 5000
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Last active /omp style is pair_style sw/mod/omp
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.158796
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ghost atom cutoff = 5.158796
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binsize = 2.579398, bins = 30 18 78
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair sw/mod/omp, perpetual
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attributes: full, newton on, omp
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pair build: full/bin/omp
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.361 | 6.361 | 6.361 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -899.28605 -929.02881 29.742759 300
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500 -899.28626 -922.45519 23.168929 233.69313
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1000 -899.29247 -925.86547 26.573002 268.02828
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1500 -899.27957 -916.95478 17.675214 178.28084
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2000 -899.28171 -918.38728 19.105573 192.70814
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2500 -899.28732 -922.50423 23.21691 234.17709
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3000 -899.28195 -918.74112 19.459174 196.27473
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3500 -899.27944 -918.03105 18.751604 189.13784
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4000 -899.28397 -920.50737 21.223397 214.06955
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4500 -899.28386 -919.79154 20.507685 206.85053
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5000 -899.28077 -918.78947 19.508698 196.77425
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Loop time of 0.703794 on 4 procs for 5000 steps with 768 atoms
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Performance: 613.816 ns/day, 0.039 hours/ns, 7104.353 timesteps/s
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99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.60288 | 0.60616 | 0.60938 | 0.3 | 86.13
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Bond | 0.00018681 | 0.00019351 | 0.00020187 | 0.0 | 0.03
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.070503 | 0.07298 | 0.077342 | 1.0 | 10.37
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Output | 0.00011523 | 0.00012677 | 0.00014986 | 0.0 | 0.02
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Modify | 0.014053 | 0.014315 | 0.014556 | 0.1 | 2.03
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Other | | 0.01002 | | | 1.42
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Nlocal: 192.000 ave 194 max 190 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Nghost: 194.000 ave 196 max 192 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 5120.00 ave 5170 max 5070 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Total # of neighbors = 20480
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Ave neighs/atom = 26.666667
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Ave special neighs/atom = 0.0000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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